Metabolic Flux-Based Modularity using Shortest Retroactive distances

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Sridharan, Gautham Vivek ^a   Yi, Michael ^a   Hassoun, Soha ^a   Lee, Kyongbum ^a  

^a Tufts University   (United States)

Author keywords

Adipocyte metabolism; Edge weighting; Metabolic flux; Metabolic networks; Modularity; Retroactivity

Indexed keywords

ENZYME INHIBITOR;

ADIPOCYTE; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CELL DIFFERENTIATION; COMPUTER GRAPHICS; CYTOLOGY; DRUG EFFECT; METABOLISM; METHODOLOGY;

ADIPOCYTES; CELL DIFFERENTIATION; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; ENZYME INHIBITORS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

MLCS; MLOWN;

EID: 84871603597     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-155     Document Type: Article

References (29)

1. Floyd RW. Algorithm-97 - Shortest Path. Commun Acm 1962, 5:345.
2. Girvan M, Newman ME. Community structure in social and biological networks. Proc Natl Acad Sci U S A 2002, 99:7821-7826. 10.1073/pnas.122653799, 122977, 12060727.
3. Zhao J, Yu H, Luo JH, Cao ZW, Li YX. Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinformatics 2006, 7:386. 10.1186/1471-2105-7-386, 1560398, 16916470.
4. Holme P, Huss M, Jeong H. Subnetwork hierarchies of biochemical pathways. Bioinformatics 2003, 19:532-538. 10.1093/bioinformatics/btg033, 12611809.
5. Papin JA, Reed JL, Palsson BO. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci 2004, 29:641-647. 10.1016/j.tibs.2004.10.001, 15544950.
6. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555. 10.1126/science.1073374, 12202830.
7. Trevino S, Sun Y, Cooper TF, Bassler KE. Robust detection of hierarchical communities from Escherichia coli gene expression data. PLoS Comput Biol 2012, 8:e1002391. 10.1371/journal.pcbi.1002391, 3285575, 22383870.
8. Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics 2004, 4:928-942. 10.1002/pmic.200300636, 15048975.
9. Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol 2012, 8:565. 3296360, 22252388.
10. Potapov AP, Goemann B, Wingender E. The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks. BMC Bioinformatics 2008, 9:227. 10.1186/1471-2105-9-227, 2396639, 18454847.
11. Tang X, Wang J, Liu B, Li M, Chen G, Pan Y. A comparison of the functional modules identified from time course and static PPI network data. BMC Bioinformatics 2011, 12:339. 10.1186/1471-2105-12-339, 3174950, 21849017.
12. Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A 2012, 109:594-599. 10.1073/pnas.1116053109, 3258644, 22184244.
13. Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 2009, 27:199-204. 10.1038/nbt.1522, 19182785.
14. Yoon J, Si Y, Nolan R, Lee K. Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection. Bioinformatics 2007, 23:2433-2440. 10.1093/bioinformatics/btm374, 17660208.
15. Si Y, Yoon J, Lee K. Flux profile and modularity analysis of time-dependent metabolic changes of de novo adipocyte formation. Am J Physiol Endocrinol Metab 2007, 292:E1637-E1646. 10.1152/ajpendo.00670.2006, 17284573.
16. Ma HW, Zhao XM, Yuan YJ, Zeng AP. Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 2004, 20:1870-1876. 10.1093/bioinformatics/bth167, 15037506.
17. Sridharan GV, Hassoun S, Lee K. Identification of biochemical network modules based on shortest retroactive distances. PLoS Comput Biol 2011, 7:e1002262. 10.1371/journal.pcbi.1002262, 3213171, 22102800.
18. Saez-Rodriguez J, Gayer S, Ginkel M, Gilles ED. Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. Bioinformatics 2008, 24:i213-i219. 10.1093/bioinformatics/btn289, 18689828.
19. Croes D, Couche F, Wodak SJ, van Helden J. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006, 356:222-236. 10.1016/j.jmb.2005.09.079, 16337962.
20. Carlisle-Moore L, Gordon CR, Machutta CA, Miller WT, Tonge PJ. Substrate recognition by the human fatty-acid synthase. J Biol Chem 2005, 280:42612-42618. 10.1074/jbc.M507082200, 2442872, 16215233.
21. Ozer N, Aksoy Y, Ogus IH. Kinetic properties of human placental glucose-6-phosphate dehydrogenase. Int J Biochem Cell Biol 2001, 33:221-226. 10.1016/S1357-2725(01)00011-5, 11311853.
22. Rippa M, Giovannini PP, Barrett MP, Dallocchio F, Hanau S. 6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species. Biochim Biophys Acta 1998, 1429:83-92. 10.1016/S0167-4838(98)00222-2, 9920387.
23. Shearer HL, Turpin DH, Dennis DT. Characterization of NADP-dependent malic enzyme from developing castor oil seed endosperm. Arch Biochem Biophys 2004, 429:134-144. 10.1016/j.abb.2004.07.001, 15313216.
24. Dervartanian DV, Veeger C. Studies on Succinate Dehydrogenase, I. Spectral Properties of the Purified Enzyme and Formation of Enzyme-Competitive Inhibitor Complexes. Biochim Biophys Acta 1964, 92:233-247.
25. Lehninger AL, Nelson DL, Cox MM. Lehninger principles of biochemistry 2005, New York: W.H. Freeman, 4.
26. Martinez-Rivas JM, Vega JM. Purification and characterization of NAD-isocitrate dehydrogenase from chlamydomonas reinhardtii. Plant Physiol 1998, 118:249-255. 10.1104/pp.118.1.249, 34862, 9733544.
27. Si Y, Shi H, Lee K. Impact of perturbed pyruvate metabolism on adipocyte triglyceride accumulation. Metab Eng 2009, 11:382-390. 10.1016/j.ymben.2009.08.001, 2783285, 19683593.
28. Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci U S A 2006, 103:8577-8582. 10.1073/pnas.0601602103, 1482622, 16723398.
29. Cormen TH. Introduction to algorithms 2009, Cambridge, Mass: MIT Press, 3.